When the technology enabling the study of molecular polymorphisms—variations in the sequences of genes and proteins—first arose, a great deal more variability was discovered in natural populations than most evolutionary biologists had expected under natural selection. The neutral theory made the bold claim that these polymorphisms become prevalent through chance alone. It sees polymorphism and long-term evolutionary change as two aspects of the same phenomenon: random changes in the frequencies of alleles. While the neutral theory does not deny that natural selection may be important in adaptive evolutionary change, it does claim that natural selection accounts for a very small fraction of genetic evolution.

A dramatic consequence now follows. Most evolutionary change at the genetic level is not adaptive.

It is difficult to imagine random changes accomplishing so much. But random genetic drift is now widely recognized as one of the most important mechanisms of evolution.

I don't think there's any doubt that this claim is correct as long as you stick to the proper definition of evolution. The vast majority of fixations of alleles are likely due to random genetic drift and not natural selection.

If you don't understand this then you don't understand evolution.

The only quibble I have with the essay is the reference to "Neutral Theory of Evolution" as the antithesis of "Darwinian Evolution" or evolution by natural selection. I think "Neutral Theory" should be restricted to the idea that many alleles are neutral or nearly neutral. These alleles can change in frequency in a population by random genetic drift. The key idea that's anti-Darwinian includes that fact plus two other important facts:

New beneficial alleles can be lost by drift before they ever become fixed. In fact, this is the fate of most new beneficial alleles. It's part of the drift-barrier hypothesis.

Detrimental alleles can occasionally become fixed in a population due to drift.

In both cases, the alleles are not neutral. The key to understanding the overall process is random genetic drift not the idea of neutral alleles—although that's also important.

Originally proposed by Motoo Kimura, Jack King, and Thomas Jukes, the neutral theory of molecular evolution is inherently non-Darwinian. Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance.

I would just add that it's Neutral Theory PLUS the other effects of random genetic drift that make evolution much more random than most people believe.

Austin Hughes was a skeptic and a creative thinker who often disagreed with the prevailing dogma in the field of evolutionary biology. He was also very religious, a fact I find very puzzling.

His scientific views were often correct, in my opinion.

In 2013, the ENCODE (Encyclopedia of DNA Elements) Project published results suggesting that eighty per cent of the human genome serves some function. This was considered a rebuttal to the widely held view that a large part of the genome was junk, debris collected over the course of evolution. Hughes sided with his friend Dan Graur in rejecting this point of view. Their argument was simple. Only ten per cent of the human genome shows signs of purifying selection, as opposed to neutrality.

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The vast majority of changes of gene frequency are due to genetic drift. However a lot of those changes are in sites in the genome that have no phenotypic consequences. In sites where there are effects on phenotype (regulatory or coding sequences) it is still true that most changes of gene frequency are due to drift. Most of that is jiggling of gene frequencies back and forth due to drift. In asking about "most changes" we are adding up the abolute values of the changes, not considering that many of them cancel each other out.

At those sites, does that establish that most net change in gene frequencies is due to drift? No!

At those sites, does that establish that most net phenotypic change is due to drift? No!

Note the difference once one focuses on net change.

In a beaker with many tiny particles slightly heavier than the liquid, most change is due to Brownian Motion. But the particles do show a tendency to settle.

Let's just consider fixation. If you compare the human and chimp genomes, what fraction of the difference is due to fixation of nearly neutral alleles by random genetic drift and what fraction is due to selection?

The situation wrt alleles that affect phenotype is controversial, as you well know. We just don't know what percentage of those alleles are effectively neutral, what percentage are detrimental, and what percentage are associated with significant selection coefficients.

The common assumption is that almost all alleles affecting phenotype are not neutral. But this is the adaptationist position that assumes, as the null hypothesis, that all phenotypes are subject to selection. That's not a valid assumption.

The main "issue" as far as I'm concerned is that most people don't know about Neutral Theory and random genetic drift. Unfortunately, that includes a great many scientists. I met some of them at a Royal Society Meeting in London last November.

I'd be happy if all scientists and most of the general public realized that there's more to evolution than natural selection.

Sorry, I was unclear. I guess I was reacting to your earlier statements, not Hughes's views. You like to say that most gene frequency change is genetic drift. True in one sense, but to what extent does that imply that drift overwhelms selection?

I think you are having an unreasonable discussion here. If I had a biased coin with a probability of .55 of getting heads and tossed it a million times getting 550,515 heads, it doesn't make sense to me to say that some of these head results are due to coin tossing, while others are due to bias. And thus it wouldn't make sense to me to ask whether more of them are due to coin tossing or the bias either. Each of them is obviously produced by the same process and thus making a difference between one head result and another does not make sense.

Each of them is obviously produced by the same process and thus making a difference between one head result and another does not make sense.

Does it make sense to you to tease out flips in which the environment may have played a role? Say you were flipping an object shaped in such a way that the wind might affect which side came up, and you were in a location where the wind was blowing during some flips and not others. Would it make sense to separate those where the wind was blowing from the others?

@Judmarc: Not in the model I gave. And there is a simple model that works like this: There is a population of N haploid organisms, some of which have allele A.We are considering pairs consisting of the next organism to reproduce and the next organism to die. In each case this leads to an increase of the allele frequency of A by 1/N, a decrease of 1/N or no change.We now ignore the instances where no change occured.THen we obtain the probability for an increase in each of the remaining steps as 1/(1+e^-s) and for a decrease of 1/(1+e^s)=1-1/(1+e^-s). I.e. we do get a biased coin toss model for evolution in that population (the simplifications we made make it bad at some things, you can't work out the mean time to fixation for instance, but it is accurate enough to figure out things like the probability of fixation for mutant alleles for instance). It's worth noting that s is the log of the mean fitness of A-type individuals divided by the mean fitness of not-A-type individuals. There might well be differences between the fitness of organisms and in the case of haploid clonal organisms these are simply twice the probability of reproduction before death. But what we are interested in is how allele frequency changes and that only depends on these mean values (for instance if there is some other locus affecting fitness and there is no LD between that locus and the one we are interested in, this would result in differences between the fitness of individuals, but we can ignore it when we look at the locus we are interested in, because these differences have nothing to do with allele A).So, if you want to go that route you end up looking at entire genomes rather than particular genes for which you want to track allele frequencies and you look at individuals, rather than populations. I would argue that at that level you can not really talk about things like selection anymore, because these are explicitly about populations. Individuals reproduce and die. And if a lot of individuals reproduce and die we can rewrite the aggregate effect of these births and deaths as selection and drift (or, as I keep on argueing, just treat them as a single resampling process).I think a while ago I had a similar discussion on a forum, where the poster argued that there were instances of selection, like a cheetah catching the slower gazelle and I pointed out that our model asks: Which of the Gazelles is the next to die. That of course also depends on none of the other Gazelles getting struck by lightning first.

In 1973, “A Random Walk Down Wall Street” was published.It makes the case that the movements in stock prices could be well modeled as a ‘random walk’ and therefore trying to use mathematics to ‘time the market’ won’t work.I believe the hypothesis has proved to be correct.

But what moves the markets are the ‘buy’ and ‘sell’ decisions of the individual investors. The person doing the buying has a reason for wanting to buy at that price, and the person doing the selling has a reason to accept the price as well.The individual decisions are not done ‘at random’, yet the conglomeration can be modeled that way.

I bring this as a possible analogy for evolution where the changes in allele frequencies can be modeled as ‘at random’, but the individual acts of reproduction and death might not fit that description so well.

@Simon Gunkel: In your coin toss example, over a very large number of trials the incidence of heads would presumably get quite close to 55%. If it stubbornly did not, I should think that might be of interest. Or to make it even more simple, if you are tossing a coin and not approaching 50% incidence of heads over a very large number of trials, you might be interested in what was causing it to come out very close to 55% instead.

True. But in my example the coin tosses were IID, which means they would converge on some value and it is easy to note that the MLE for the probability of getting heads is simply the number of heads divided by the number of tosses and that we can fit confidence intervals around these rather easily as well. If in the simplified moran model we had some number of increases vs. some number of decreases we could perform statistical tests to check whether we could rule out neutrality (s=0) with any confidence. We could compare this to some other allele and check things like whether the respective selection coefficients are significantly different from one another.

What a creationist can draw from these corrective ideas in the subjecty of evolutionary biology is as follows.First a wrong idea would of prevailed until superior investigative tactics were made.(study/molecular polymorphisms. A original error in evolutionism is always a option.Second. The correction overthrows natural selection at the genetic level. this because natural selection does not work at that level they now decided.It means as better investigation takes place, at a more atomic level, in real time, Darwins evolution ideas oncve again come up short. so new ideas are needed to save the day. Like stephen goulds attempt to save the fossil record for evidence of evolutionary change. He gave up a little to save a lot. it failed but he knew there was a serious problem.

So from these things a creationist can draw a deeper philosophy about scientific investigation and so conclusions..Without having a competence to deal with the subject at a high or even entry level status.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.